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A reference guide to Wikidata

A reference guide to Wikidata and its connection to OBO

Introduction to Wikidata

OBO in Wikidata


On Wikidata the following licenses applies:

"All structured data from the main, Property, Lexeme, and EntitySchema namespaces is available under the Creative Commons CC0 License; text in the other namespaces is available under the Creative Commons Attribution-ShareAlike License"

Adding non-CC0 licensed OBO ontologies in full might be problematic due to * License stacking

IANL, but my understanding is that as long as only URI mappings are created to OBO ontology terms no licenses are breached (even if the ontology is not CC0)

Why map OBO uris to Wikidata?

  • Wikidata is a hub in the Linked Open Data cloud; it is, thus, a good place to crowdsource database cross references (e.g. between the Cell Ontology and FMA).
  • Wikidata provides direct links between items and Wikipedia, as well as a proxy for how many different Wikipedia languages are available for each concept. These can be acessed via SPARQL queries (e.g Wikipedia links are useful for adding explainability to applications, and language count can be a proxy for popularity of concepts.
    • E.g. The top popular concepts with a CL ID are "Cell", "Red Blood Cell" and "Neuron" with over 100 Wikipedia languages each (
  • Wikidata is multilingual and most (if not all) OBO ontologies are English-only. Wikidata provides infrastructure to record preferred labels accross 200+ languages (not sure the current number).

Notable differences

  • Wikidata's model is definition-free. The meaning of Wikidata terms by a combination of the label, description, aliases and statements.
  • Wikidata does not support reasoning, as supporting inconsistencies are a feature (not a bug). It is so to handle knowledge diversity.